
def config = new ConfigSlurper().parse(new File('scripts/1_upload_proteins_ipi.conf').toURL())

//sets the Services in the Upload class, to make them available
def uploadService = ctx.getBean("uploadService")

//get the organism
println 'prepare organism...'
def organism = uploadService.getOrganism(config.organism)

println 'prepare for uploading proteins...'
uploadService.uploadProteins(new File(config.proteins.datFile), organism, config.proteins.outputFolder, new File(config.proteins.uniprotIdFile), config.proteins.upload.toBoolean())
